Abstract:

Objective The stipe of Pleurotus cornucopiae strain CCMSSC 04611 is short, thick and hard, and the cap color is dark. However, the molecular mechanism of the formation of short stipe is still unclear. The whole genome of CCMSSC 04611 was sequenced and assembled, then compared with the genome of P. cornucopiae with long stipe to analyze the genome composition, genetic variation and reasons for the formation of short stipe. Method Extract the genomic DNA of P. cornucopiae CCMSSC 04611, which was used to perform genome sequencing, assembly, and annotation through the second-generation Illumina and the third-generation pacbio sequencing platform. Then compare the genomic differences and morphological characteristics between the genome of CCMSSC 04611 and the P. cornucopiae with long stipe. Result Total 8.3 Gb raw reads of CCMSSC 04611 were obtained through second-generation sequencing, and about 8.29 Gb of clean reads were obtained after filtering out low-quality sequences. Total 7.42 Gb of raw reads of CCMSSC 04611 were obtained through third-generation sequencing and assembly, of which about 7.416 Gb was clean reads after filtering out low-quality sequences. The genome GC content of CCMSSC 04611 was 50.85%, and the number of gaps was 0. Combining second- and third-generation sequencing data, a total of 23 contigs longer than 1 kb were obtained from the CCMSSC 04611 genome, with a total length of 34 635 218 bp. The quality of this genome was evaluated by the proportion of second-generation sequencing data aligned to the assembled genome and busco evaluation. The results confirmed that the assembled genome were reliable. Functional annotation of predictive coding genes showed that a total of 9 999 genes were annotated, of which 6 331 and 3 052 genes were annotated in GO and KEGG databases, respectively. Compared the assembled genome with the P. cornucopiae CCMSSC 00406, the number of shared gene families accounted for more than 98.33% and the proportion of shared functional genes was higher than 83.97%. There were 124 unique gene families with 1 618 unique functional genes in CCMSSC 04611, which were enriched in cellular components, catalytic activities, transcription factors, protein synthesis, MAPK signal transduction, and other biological processes. Conclusion High-quality genome reference data for CCMSSC 04611 were obtained by the Illumina and pacbio revio sequencing platforms. Differences were found between the genome of CCMSSC 04611 and the Pleurotus cornucopiae CCMSSC 00406 with long stipe, providing a theoretical basis for further research for the molecular mechanisms of the short stipe formation of CCMSSC 04611.

Key words: Pleurotus cornucopiae, whole genome sequencing, function annotation, stipe length, comparative genomic analysis